/*
 * Copyright (c) 2021 Quim Aguado
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy of
 * this software and associated documentation files (the "Software"), to deal in
 * the Software without restriction, including without limitation the rights to
 * use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
 * the Software, and to permit persons to whom the Software is furnished to do so,
 * subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in all
 * copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
 * FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
 * COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
 * IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
 * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */

#ifndef ALIGNMENT_RESULTS_H
#define ALIGNMENT_RESULTS_H

#include "wfa_types.h"
#include <stdbool.h>
#include <stddef.h>
#include <stdlib.h>

typedef struct {
    char* buffer;
    size_t buffer_size;
    size_t last_free_position;
} wfa_cigar_t;

// Internal structure (produced by the kernel)
typedef struct {
    bool finished;
    int distance;
    wfa_backtrace_t backtrace;
    int num_bt_blocks;
} alignment_result_t;

// Public API structure
typedef struct {
    unsigned int error;
    wfa_cigar_t cigar;
} wfa_alignment_result_t;

#ifdef __cplusplus
extern "C"{
#endif

bool initialize_wfa_results (wfa_alignment_result_t** results,
                             const size_t num_alignments,
                             const size_t cigar_length);

bool destroy_wfa_results (wfa_alignment_result_t* results,
                             const size_t num_alignments);

#ifdef __cplusplus
}
#endif

#endif
